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This page was generated on 2022-10-19 13:23:23 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for NormalyzerDE on merida1


To the developers/maintainers of the NormalyzerDE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NormalyzerDE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1335/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NormalyzerDE 1.14.0  (landing page)
Jakob Willforss
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/NormalyzerDE
git_branch: RELEASE_3_15
git_last_commit: b459349
git_last_commit_date: 2022-04-26 11:50:51 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NormalyzerDE
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NormalyzerDE_1.14.0.tar.gz
StartedAt: 2022-10-19 05:32:32 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:43:08 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 635.7 seconds
RetCode: 0
Status:   OK  
CheckDir: NormalyzerDE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NormalyzerDE_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/NormalyzerDE.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NormalyzerDE/DESCRIPTION’ ... OK
* this is package ‘NormalyzerDE’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘NormalyzerDE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
generatePlots                 27.972  0.754  28.782
NormalyzerEvaluationResults    9.498  0.247   9.758
writeNormalizedDatasets        8.829  0.040   8.896
analyzeNormalizations          8.723  0.048   8.785
getSmoothedRTNormalizedMatrix  6.178  0.071   6.261
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/NormalyzerDE.Rcheck/00check.log’
for details.



Installation output

NormalyzerDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NormalyzerDE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘NormalyzerDE’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NormalyzerDE)

Tests output

NormalyzerDE.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(NormalyzerDE)
> test_check("NormalyzerDE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
 60.044   1.167  61.280 

Example timings

NormalyzerDE.Rcheck/NormalyzerDE-Ex.timings

nameusersystemelapsed
NormalyzerEvaluationResults9.4980.2479.758
NormalyzerResults0.1690.0020.171
NormalyzerStatistics0.0280.0010.030
analyzeNormalizations8.7230.0488.785
calculateContrasts0.1780.0040.183
generateAnnotatedMatrix0.0960.0020.098
generatePlots27.972 0.75428.782
generateStatsReport4.2170.0304.261
getRTNormalizedMatrix2.8300.0532.889
getSmoothedRTNormalizedMatrix6.1780.0716.261
getVerifiedNormalyzerObject0.0760.0010.079
globalIntensityNormalization0.0070.0010.008
loadData000
loadDesign0.0000.0000.001
meanNormalization0.0070.0010.008
medianNormalization0.0070.0020.008
normMethods3.4080.0193.432
normalyzer0.0000.0000.001
normalyzerDE1.9410.0522.014
performCyclicLoessNormalization0.0120.0010.013
performGlobalRLRNormalization0.0300.0010.031
performQuantileNormalization0.0020.0010.002
performSMADNormalization0.0030.0010.005
performVSNNormalization0.0370.0020.038
reduceTechnicalReplicates0.0550.0010.055
setupJobDir0.0000.0000.001
setupRawContrastObject0.0240.0000.025
setupRawDataObject0.0320.0010.033
setupTestData0.0020.0000.002
writeNormalizedDatasets8.8290.0408.896